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- PDB-8zl8: Structure of Polycystin-1/Polycystin-2 complex with 7b,27-DHC -

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Basic information

Entry
Database: PDB / ID: 8zl8
TitleStructure of Polycystin-1/Polycystin-2 complex with 7b,27-DHC
Components
  • Polycystin-1
  • Polycystin-2
KeywordsMEMBRANE PROTEIN / ion channel
Function / homology
Function and homology information


metanephric distal tubule morphogenesis / nitrogen cycle metabolic process / detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development ...metanephric distal tubule morphogenesis / nitrogen cycle metabolic process / detection of nodal flow / metanephric smooth muscle tissue development / metanephric cortex development / metanephric cortical collecting duct development / metanephric distal tubule development / polycystin complex / mesonephric tubule development / mesonephric duct development / metanephric part of ureteric bud development / renal tubule morphogenesis / determination of liver left/right asymmetry / lung epithelium development / metanephric ascending thin limb development / lymph vessel morphogenesis / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / basal cortex / renal artery morphogenesis / mitocytosis / metanephric proximal tubule development / HLH domain binding / calcium-induced calcium release activity / calcium-independent cell-matrix adhesion / Wnt receptor activity / cilium organization / VxPx cargo-targeting to cilium / genitalia development / migrasome / muscle alpha-actinin binding / detection of mechanical stimulus / regulation of calcium ion import / voltage-gated monoatomic ion channel activity / placenta blood vessel development / cellular response to hydrostatic pressure / Golgi-associated vesicle membrane / response to fluid shear stress / cellular response to fluid shear stress / metanephric collecting duct development / cation channel complex / outward rectifier potassium channel activity / non-motile cilium / cartilage development / cellular response to osmotic stress / actinin binding / determination of left/right symmetry / digestive tract development / : / voltage-gated monoatomic cation channel activity / neural tube development / voltage-gated sodium channel activity / aorta development / motile cilium / branching involved in ureteric bud morphogenesis / ciliary membrane / cartilage condensation / skin development / protein heterotetramerization / branching morphogenesis of an epithelial tube / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / heart looping / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytoplasmic side of endoplasmic reticulum membrane / establishment of cell polarity / homophilic cell-cell adhesion / centrosome duplication / regulation of G1/S transition of mitotic cell cycle / voltage-gated potassium channel activity / lateral plasma membrane / anatomical structure morphogenesis / cell surface receptor signaling pathway via JAK-STAT / potassium channel activity / embryonic placenta development / regulation of cell adhesion / monoatomic cation channel activity / voltage-gated calcium channel activity / transcription regulator inhibitor activity / cytoskeletal protein binding / release of sequestered calcium ion into cytosol / potassium ion transmembrane transport / regulation of proteasomal protein catabolic process / calcium channel complex / cellular response to calcium ion / sodium ion transmembrane transport / basal plasma membrane / protein export from nucleus / cellular response to cAMP / cytoplasmic vesicle membrane / regulation of mitotic spindle organization / cell-matrix adhesion / cellular response to reactive oxygen species / protein tetramerization / lumenal side of endoplasmic reticulum membrane / kidney development / phosphoprotein binding / establishment of localization in cell / liver development / peptidyl-serine phosphorylation
Similarity search - Function
Polycystic kidney disease type 1 protein / PKD/REJ-like domain / Polycystin cation channel / REJ domain / REJ domain / REJ domain profile. / Polycystin-1 like, PLAT/LH2 domain / Carbohydrate-binding WSC / WSC domain / WSC domain profile. ...Polycystic kidney disease type 1 protein / PKD/REJ-like domain / Polycystin cation channel / REJ domain / REJ domain / REJ domain profile. / Polycystin-1 like, PLAT/LH2 domain / Carbohydrate-binding WSC / WSC domain / WSC domain profile. / present in yeast cell wall integrity and stress response component proteins / Ferredoxin I 4Fe-4S cluster domain / : / Polycystic kidney disease type 2 protein / Polycystin domain / PKD domain / Polycystin domain / Lipoxygenase homology 2 (beta barrel) domain / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / Polycystic kidney disease (PKD) domain profile. / : / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Polycystin cation channel, PKD1/PKD2 / Polycystin cation channel / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Voltage-dependent channel domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Polycystin-1 / Polycystin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.38 Å
AuthorsChen, M.Y. / Su, Q. / Shi, Y.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: To Be Published
Title: Structure of Polycystin-1/Polycystin-2 complex with 7b,27-DHC
Authors: Chen, M.Y. / Su, Q. / Shi, Y.G.
History
DepositionMay 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polycystin-1
B: Polycystin-2
C: Polycystin-2
D: Polycystin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,92611
Polymers479,1804
Non-polymers1,7467
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Polycystin-1 / PC1 / Autosomal dominant polycystic kidney disease 1 protein


Mass: 138514.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD1 / Production host: Homo sapiens (human) / References: UniProt: P98161
#2: Protein Polycystin-2 / PC2 / Autosomal dominant polycystic kidney disease type II protein / Polycystic kidney disease 2 ...PC2 / Autosomal dominant polycystic kidney disease type II protein / Polycystic kidney disease 2 protein / Polycystwin / R48321 / Transient receptor potential cation channel subfamily P member 2


Mass: 113555.008 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKD2, TRPP2 / Production host: Homo sapiens (human) / References: UniProt: Q13563
#3: Chemical ChemComp-A1EQ3 / (3~{S},7~{R},8~{S},9~{S},10~{R},13~{R},14~{S},17~{R})-10,13-dimethyl-17-[(2~{R},6~{R})-6-methyl-7-oxidanyl-heptan-2-yl]-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthrene-3,7-diol / 7beta,27-Dihydroxycholesterol


Mass: 418.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O3
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of Polycystin-1/Polycystin-2 complex with 7b,27-DHC
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118205 / Symmetry type: POINT

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